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(-) Description

Title :  CRYSTAL STRUCTURE OF UNCHARACTERIZED PROTEIN PSPTO_3204 FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000
 
Authors :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New Y Research Center For Structural Genomics (Nysgxrc)
Date :  05 Oct 09  (Deposition) - 13 Oct 09  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Crystal Structure, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Uncharacterized Protein Pspto_3204 Fro Pseudomonas Syringae Pv. Tomato Str. Dc3000
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AAO56687.1, PSPTO3204
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. TOMATO
    Organism Taxid: 323
    Strain: DC3000

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG3Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:200 , HOH A:309 , ASP B:102 , HOH B:252 , HOH B:255 , HOH B:308BINDING SITE FOR RESIDUE MG B 501
2AC2SOFTWAREGLY A:101 , ILE A:103 , MSE A:104BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREGLU B:200 , HOH B:267 , HOH B:270 , ASP C:102 , HOH C:248 , HOH C:274BINDING SITE FOR RESIDUE MG C 501
4AC4SOFTWAREGLY B:101 , ILE B:103 , MSE B:104 , HOH B:371BINDING SITE FOR RESIDUE CL B 502
5AC5SOFTWAREASP A:102 , HOH A:245 , HOH A:303 , GLU C:200 , HOH C:325 , HOH C:326BINDING SITE FOR RESIDUE MG A 501
6AC6SOFTWAREGLY C:101 , ILE C:103 , MSE C:104BINDING SITE FOR RESIDUE CL C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K4I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K4I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K4I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K4I)

(-) Exons   (0, 0)

(no "Exon" information available for 3K4I)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:202
 aligned with Q880F6_PSESM | Q880F6 from UniProtKB/TrEMBL  Length:237

    Alignment length:212
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214  
         Q880F6_PSESM     5 FEYTPIAQSVLDECEHLDTASLSDALDSLGIDGGLPGIASQVPGTRCVGIAFTVQYQPVDASEGFRGAANYIDQVPSGSVIVSSNSGRHDCTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFMQSAKNRTQLKAVQVPLVIDGITIQPGDLMVCDGSGCVVVPQQLAAEVVLRARAVEQTERRIIEAISSGSTLEQARM 216
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh..hhhhhhhhhhhh.........ee......eeeeeeeeeeee.----------hhhhhh...eeeeee..........hhhhhhhhhhh...eeeee....hhhhhhhh...eee...........eeeeee...eee..eee....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4i A   7 FEYTPIAQSVLDECEHLDTASLSDALDSLGIDGGLPGIASQVPGTRCVGIAFTVQYQPV----------NYIDQVPSGSVIVSSNSGRHDCTVWGDImTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFmQSAKNRTQLKAVQVPLVIDGITIQPGDLmVCDGSGCVVVPQQLAAEVVLRARAVEQTERRIIEAISSGSTLEQARm 218
                                    16        26        36        46        56        |-        76        86        96       106       116       126       136     | 146       156       166    |  176       186       196       206       216 |
                                                                                     65         76                         104-MSE                               142-MSE                      171-MSE                                        218-MSE


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with Q880F6_PSESM | Q880F6 from UniProtKB/TrEMBL  Length:237

    Alignment length:210
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
         Q880F6_PSESM     7 YTPIAQSVLDECEHLDTASLSDALDSLGIDGGLPGIASQVPGTRCVGIAFTVQYQPVDASEGFRGAANYIDQVPSGSVIVSSNSGRHDCTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFMQSAKNRTQLKAVQVPLVIDGITIQPGDLMVCDGSGCVVVPQQLAAEVVLRARAVEQTERRIIEAISSGSTLEQARM 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhh..hhhhhhhhhhhh.........ee......eeeeeeeeeeee.----------hhhhhh...eeeeee..........hhhhhhhhhhh...eeeee....hhhhhhhh...eee...........eeeeee...eee..eee....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k4i B   9 YTPIAQSVLDECEHLDTASLSDALDSLGIDGGLPGIASQVPGTRCVGIAFTVQYQPV----------NYIDQVPSGSVIVSSNSGRHDCTVWGDImTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFmQSAKNRTQLKAVQVPLVIDGITIQPGDLmVCDGSGCVVVPQQLAAEVVLRARAVEQTERRIIEAISSGSTLEQARm 218
                                    18        28        38        48        58      |  -       |78        88        98     | 108       118       128       138   |   148       158       168  |    178       188       198       208       218
                                                                                   65         76                         104-MSE                               142-MSE                      171-MSE                                        218-MSE


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with Q880F6_PSESM | Q880F6 from UniProtKB/TrEMBL  Length:237

    Alignment length:219
                             1                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
         Q880F6_PSESM     - -MSVPFEYTPIAQSVLDECEHLDTASLSDALDSLGIDGGLPGIASQVPGTRCVGIAFTVQYQPVDASEGFRGAANYIDQVPSGSVIVSSNSGRHDCTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFMQSAKNRTQLKAVQVPLVIDGITIQPGDLMVCDGSGCVVVPQQLAAEVVLRARAVEQTERRIIEAISSGSTLEQARMTY 218
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------Methyltransf_6-3k4iC01 C:21-180                                                                                                                                 ---------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------Methyltransf_6-3k4iC02 C:21-180                                                                                                                                 ---------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------Methyltransf_6-3k4iC03 C:21-180                                                                                                                                 ---------------------------------------- Pfam domains (3)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..........ee......eeeeeeeeeee.....------hhhhhhh...eeeeee..........hhhhhhhhhhh...eeeee....hhhhhhhh...eee............eeeee...eee..eee....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4i C   2 SLSVPFEYTPIAQSVLDECEHLDTASLSDALDSLGIDGGLPGIASQVPGTRCVGIAFTVQYQPVDAS------ANYIDQVPSGSVIVSSNSGRHDCTVWGDImTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFmQSAKNRTQLKAVQVPLVIDGITIQPGDLmVCDGSGCVVVPQQLAAEVVLRARAVEQTERRIIEAISSGSTLEQARmTY 220
                                    11        21        31        41        51        61      |  -   |    81        91       101  |    111       121       131       141|      151       161       171       181       191       201       211      |  
                                                                                             68     75                          104-MSE                               142-MSE                      171-MSE                                        218-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3K4I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K4I)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Methyltransf_6] (5)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q880F6_PSESM | Q880F6)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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